The present invention is in the technical field of agricultural food animal production. More particularly, the invention relates to poultry waste management and, specifically, to fumigation of a commercial poultry housing unit that is equipped with a ventilated plenum flooring system. A properly installed and operated ventilated plenum flooring system eliminates the need for bedding material and facilitates manure removal immediately after collection of each market ready flock. However, widely accepted industry practice requires at least fourteen full days of “layout time” to lower airborne ammonia concentrations and reduce housing unit microbial pathogens through fresh air ventilation for an extended period before a poultry housing unit is restocked with a new poultry flock. Conventional practice overlooks the potential benefits of a ventilated flooring system with just-in-time manure cleanout and fumigation after each flock, virtually eliminating ammonia and achieving managed reduction of pathogens within a brief time interval. The reduction of flock cycle time through just-in-time manure removal and managed pathogen reduction allows increased operational efficiency while also reducing adverse environmental, public nuisance and potential health impact from commercial meat poultry production.